Dear all,

i am still novice in the bioinformatics journey, hence i would really appreciate any help

i noticed that when i convert my VCF file to gen using bcftools as required by IMPUTE2, the vcf ID value changes. like for example, in the VCF file i have a position with ID rs9680770. the output gen file provided by bcftools doesnt have it and it is also not present in the info file generated by IMPUTE2 !!

i need to be able to have some common value to evaluate what has been imputed out of the target used, and what has been imputed using the reference panel. the rs_is and snp_id value in the info file i cannot relate them back to the target or reference file, because as i said the ID seams to be different!!!

my next step is to exclude some SNPs using plink and run the imputation to compare with the ground truth.

hence, the aim is to find a common ground to identify and use SNPs across plink, bcftools, and IMPUTE2